Fast tool to build the core genome of prokaryotic genomes. Can handle large datasets. Dependencis: Usearch & Numpy
☆10Nov 26, 2025Updated 11 months ago
Alternatives and similar repositories for CoreCruncher
Users that are interested in CoreCruncher are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Metabolic scanning and annotation of Metagenomes☆10Dec 18, 2025Updated 10 months ago
- Assessing the quality of prokaryotic genomes, filtering and dereplication☆10Aug 26, 2022Updated 4 years ago
- metagenome population recombination rate estimation pipeline☆12Nov 23, 2025Updated 11 months ago
- R package for computing alpha and beta contributional diversity metrics☆11May 5, 2023Updated 3 years ago
- Utility to analyse a group of closely related MAgs/Genomes/bins/SUBs of more or less dubious origin☆15Sep 24, 2024Updated 2 years ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- A Snakemake workflow for recovery of plastid genomes from metagenomic samples☆11Nov 16, 2024Updated last year
- Grabbing genome accessions & download info based on taxonomy, using the NCBI REST API, w00t☆12Feb 23, 2025Updated last year
- MetagenOmic read Re-Assigner and abundance quantifier☆22Jun 24, 2026Updated 4 months ago
- Gupta et al., TaxiBGC: a Taxonomy-guided Approach for Profiling Experimentally Characterized Microbial Biosynthetic Gene Clusters and Sec…☆16May 24, 2023Updated 3 years ago
- PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.☆63May 5, 2026Updated 5 months ago
- This repository releases the model weights of ANNA16, an end-to-end tool that predicts 16S rRNA gene copy number (GCN) from 16S rRNA sequ…☆12Updated this week
- Mandrake 🌿/👨🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding☆41Aug 7, 2026Updated 2 months ago
- Pipeline for identification of eukaryotic contigs in metagenomic assemblies☆14Mar 14, 2024Updated 2 years ago
- ContScout sequence contamination filter tool☆26Dec 28, 2025Updated 10 months ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- A pipeline for whole genome assembly☆18Apr 21, 2022Updated 4 years ago
- zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)☆73Aug 27, 2026Updated 2 months ago
- ☆14Oct 29, 2024Updated 2 years ago
- Microbial Phenotype Prediction, successor to PICA, implemented with Python 3.7 and scikit-learn☆13Sep 10, 2021Updated 5 years ago
- Protologgger is a tool for the description of novel taxa by providing taxonomic, functional and ecological insights☆17Nov 24, 2025Updated 11 months ago
- A Python implementation of the OrthoANI algorithm for nucleotide identity measurement.☆38Jul 21, 2025Updated last year
- MAGqual is a command line tool to evaluate the quality of metagenomic bins and generate recommended metadata in line with the MIMAG stand…☆16Aug 28, 2024Updated 2 years ago
- ☆15Oct 14, 2023Updated 3 years ago
- ☆27Jun 20, 2023Updated 3 years ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆34Dec 4, 2025Updated 10 months ago
- Target / Integrative Genetic Element Retriever: precisely maps IGEs (a defined type of genomic island) in bacterial and archaeal genomes;…☆20Sep 2, 2025Updated last year
- Prediction of microbial interactions in complex communities☆14Aug 14, 2024Updated 2 years ago
- MICROPHERRET: MICRObial PHEnotypic tRait ClassifieR using machine lEarning Techniques☆15Oct 25, 2026Updated last week
- ☆18Jun 5, 2026Updated 4 months ago
- A platform for targeted annotation of (meta)genomic and (meta)transcriptomic datasets using HMM sets.☆20Aug 7, 2026Updated 2 months ago
- Workflow to assign Taxonomy to a bacteriophage genome isolate☆42Apr 20, 2026Updated 6 months ago
- (a) (p)erfect (c)ircle? ... tests DNA sequences for overlapping ends, then trims and rejoins, and aligns reads to test the join☆11Apr 29, 2021Updated 5 years ago
- Fast and haplotype-aware assembler☆16Oct 20, 2026Updated last week
- End-to-end encrypted cloud storage - Proton Drive • AdSpecial offer: 40% Off Yearly / 80% Off First Month. Protect your most important files, photos, and documents from prying eyes.
- Toolchest Python client☆15Sep 6, 2023Updated 3 years ago
- A mathematically characterized hypothesis test for organism presence/absence in a metagenome☆38Updated this week
- Embedding-based indexing for compact storage and rapid querying of bacterial pan-genomes☆25Sep 27, 2026Updated last month
- How many distinct k-mers are there in a sequence?☆11Oct 26, 2026Updated last week
- Pipeline for Reproducible and Scalable Integration of Metagenomic and Metatranscriptomic Data☆19Oct 7, 2026Updated 3 weeks ago
- Clustering the NCBI nr database with mmseq2 (90% length, 90% identity). Inspired by the NCBI's experimental ClusteredNR database.☆22Nov 7, 2025Updated 11 months ago
- Tool for unsupervised contig binning from viral metagenomes☆18Oct 22, 2021Updated 5 years ago